While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-ofconcept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.

Targeting the coding genome to introduce nucleotide deletions/insertions via the CRISPR/Cas9 technology has become a standard procedure. It has quickly spawned a multitude of methods such as prime editing, APEX proximity labeling, or homology directed repair, for which supporting bioinformatics tools are, however, lagging behind. New CRISPR/Cas9 applications often require specific gRNA design functionality, and a generic tool is critically missing. Here, we introduce multicrispr, an R/bioconductor tool, intended to design individual gRNAs and complex gRNA libraries. The package is easy to use; detects, scores, and filters gRNAs on both efficiency and specificity; visualizes and aggregates results per target or CRISPR/Cas9 sequence; and finally returns both genomic ranges and sequences of gRNAs. To be generic, multicrispr defines and implements a genomic arithmetic framework as a basis for facile adaptation to techniques recently introduced such as prime editing or yet to arise. Its performance and design concepts such as target set–specific filtering render multicrispr a tool of choice when dealing with screening-like approaches.

MotivationHigh throughput (HT) screens in the omics field are typically analyzed by automated pipelines that generate static visualizations and comprehensive spreadsheet data for scientists. However, exploratory and hypothesis driven data analysis are key aspects of the understanding of biological systems, both generating extensive need for customized and dynamic visualization.ResultsHere we describe WIlsON, an interactive workbench for analysis and visualization of multi-omics data. It is primarily intended to empower screening platforms to offer access to pre-calculated HT screen results to the non-computational scientist. Facilitated by an open file format, WIlsON supports all types of omics screens, serves results via a web-based dashboard, and enables end users to perform analyses and generate publication-ready plots.Availability and implementationWe implemented WIlsON in R with a focus on extensibility using the modular Shiny and Plotly frameworks. A demo of the interactive workbench without limitations may be accessed at http://loosolab.mpi-bn.mpg.de. A standalone Docker container as well as the source code of WIlsON are freely available from our Docker hub https://hub.docker. com/r/loosolab/wilson, CRAN https://cran.r-project.org/web/packages/wilson/, and GitHub repository https://github.molgen.mpg.de/loosolab/wilson-apps, respectively.

Targeting the coding genome to introduce single nucleotide deletions/insertions via Crispr/Cas9 technology has become a standard procedure in recent years. It has quickly spawned a multitude of methods such as Prime Editing, Crispr/Cas9 assisted APEX proximity labeling of proteins, or homology directed repair (HDR), for which supporting bioinformatic tools are, however, lagging behind. New applications often require specific guide-RNA (gRNA) design functionality, and a generic gRNA design tool is critically missing. Here we review gRNA designer software and introduce multicrispr, an R based tool intended to design individual gRNAs as well as gRNA libraries targeting many genomic loci in parallel. The package is easy to use, detects, scores and filters gRNAs on both efficiency and specificity, visualizes and aggregates results per target or Crispr/Cas9 sequence, and finally returns both genomic ranges as well as sequences of preferred, off target-free gRNAs. In order to be generic, multicrispr defines and implements a genomic arithmetics framework as a basis for facile adaptation to techniques yet to arise. Its performance and new gRNA design concepts such as target set specific filtering for gRNA libraries render multicrispr the tool of choice when dealing with screening-like approaches.